/usr/share/bauble/plugins/plants/family.py is in bauble 0.9.7-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# Family table definition
#
import os
import traceback
import gtk
from sqlalchemy import *
from sqlalchemy.orm import *
from sqlalchemy.orm.session import object_session
from sqlalchemy.exc import SQLError
from sqlalchemy.ext.associationproxy import association_proxy
import bauble
import bauble.db as db
import bauble.pluginmgr as pluginmgr
import bauble.editor as editor
import bauble.utils.desktop as desktop
from datetime import datetime
import bauble.utils as utils
from bauble.utils.log import debug
from bauble.types import Enum
from bauble.prefs import prefs
def edit_callback(value):
"""
Family context menu callback
"""
e = FamilyEditor(model=value)
return e.start() != None
def add_genera_callback(value):
"""
Family context menu callback
"""
e = GenusEditor(model=Genus(family=value))
return e.start() != None
def remove_callback(family):
"""
The callback function to remove a family from the family context menu.
"""
from bauble.plugins.plants.genus import Genus
session = bauble.Session()
ngen = session.query(Genus).filter_by(family_id=family.id).count()
safe_str = utils.xml_safe_utf8(str(family))
if ngen > 0:
msg = _('The family <i>%s</i> has %s genera. Are you sure you want '
'to remove it?') % (safe_str, ngen)
else:
msg = _("Are you sure you want to remove the family <i>%s</i>?") \
% safe_str
if not utils.yes_no_dialog(msg):
return
try:
obj = session.query(Family).get(family.id)
session.delete(obj)
session.commit()
except Exception, e:
msg = _('Could not delete.\n\n%s') % utils.xml_safe_utf8(e)
utils.message_details_dialog(msg, traceback.format_exc(),
type=gtk.MESSAGE_ERROR)
finally:
session.close()
return True
family_context_menu = [(_('Edit'), edit_callback),
('--', None),
(_('Add genera'), add_genera_callback),
('--', None),
(_('Remove'), remove_callback)]
def family_markup_func(family):
"""
return a string or object with __str__ method to use to markup
text in the results view
"""
return family
#
# Family
#
class Family(db.Base):
"""
:Table name: family
:Columns:
*family*:
The name if the family. Required.
*qualifier*:
The family qualifier.
Possible values:
* s. lat.: aggregrate family (senso lato)
* s. str.: segregate family (senso stricto)
* '': the empty string
*notes*:
Free text notes about the family.
:Properties:
*synonyms*:
An association to _synonyms that will automatically
convert a Family object and create the synonym.
:Constraints:
The family table has a unique constraint on family/qualifier.
"""
__tablename__ = 'family'
__table_args__ = (UniqueConstraint('family', 'qualifier'), {})
__mapper_args = {'order_by': ['family', 'qualifier']}
# columns
family = Column(String(45), nullable=False, index=True)
# we use the blank string here instead of None so that the
# contrains will work properly,
qualifier = Column(Enum(values=['s. lat.', 's. str.', '']), default=u'')
notes = Column(UnicodeText)
# relations
synonyms = association_proxy('_synonyms', 'synonym')
genera = relation('Genus', backref='family', cascade='all, delete-orphan')
_synonyms = relation('FamilySynonym',
primaryjoin='FamilySynonym.family_id==Family.id',
cascade='all, delete-orphan', uselist=True,
backref='family')
# this is a dummy relation, it is only here to make cascading work
# correctly and to ensure that all synonyms related to this family
# get deleted if this family gets deleted
__syn = relation('FamilySynonym',
primaryjoin='FamilySynonym.synonym_id==Family.id',
cascade='all, delete-orphan', uselist=True)
def __str__(self):
return Family.str(self)
@staticmethod
def str(family, qualifier=False):
if family.family is None:
return repr(family)
else:
return ' '.join([s for s in [family.family,
family.qualifier] if s not in (None,'')])
class FamilySynonym(db.Base):
"""
:Table name: family_synonyms
:Columns:
*family_id*:
*synonyms_id*:
:Properties:
*synonyms*:
*species*:
"""
__tablename__ = 'family_synonym'
__table_args__ = (UniqueConstraint('family_id', 'synonym_id'), {})
# columns
family_id = Column(Integer, ForeignKey('family.id'), nullable=False)
synonym_id = Column(Integer, ForeignKey('family.id'), nullable=False)
# relations
synonym = relation('Family', uselist=False,
primaryjoin='FamilySynonym.synonym_id==Family.id')
def __init__(self, synonym=None, **kwargs):
# it is necessary that the first argument here be synonym for
# the Family.synonyms association_proxy to work
self.synonym = synonym
super(FamilySynonym, self).__init__(**kwargs)
def __str__(self):
return Family.str(self.synonym)
#
# late imports
#
from bauble.plugins.plants.genus import Genus, GenusEditor
class FamilyEditorView(editor.GenericEditorView):
syn_expanded_pref = 'editor.family.synonyms.expanded'
_tooltips = {
'fam_family_entry': _('The family name'),
'fam_qualifier_combo': _('The family qualifier helps to remove '
'ambiguities that might be associated with '
'this family name'),
'fam_notes_textview': _('Miscelleanous notes about this family.'),
'fam_syn_box': _('A list of synonyms for this family.\n\nTo add a '
'synonym enter a family name and select one from the '
'list of completions. Then click Add to add it to '\
'the list of synonyms.')
}
def __init__(self, parent=None):
super(FamilyEditorView, self).__init__(os.path.join(paths.lib_dir(),
'plugins', 'plants',
'editors.glade'),
parent=parent)
self.dialog = self.widgets.family_dialog
self.dialog.set_transient_for(parent)
self.attach_completion('fam_syn_entry')#, self.syn_cell_data_func)
self.set_accept_buttons_sensitive(False)
self.connect_dialog_close(self.widgets.family_dialog)
self.restore_state()
def save_state(self):
prefs[self.syn_expanded_pref] = \
self.widgets.fam_syn_expander.get_expanded()
def restore_state(self):
expanded = prefs.get(self.syn_expanded_pref, True)
self.widgets.fam_syn_expander.set_expanded(expanded)
def get_window(self):
'''
'''
return self.widgets.family_dialog
def set_accept_buttons_sensitive(self, sensitive):
self.widgets.fam_ok_button.set_sensitive(sensitive)
self.widgets.fam_ok_and_add_button.set_sensitive(sensitive)
self.widgets.fam_next_button.set_sensitive(sensitive)
def start(self):
return self.dialog.run()
class FamilyEditorPresenter(editor.GenericEditorPresenter):
widget_to_field_map = {'fam_family_entry': 'family',
'fam_qualifier_combo': 'qualifier',
'fam_notes_textview': 'notes'}
def __init__(self, model, view):
'''
@param model: should be an instance of class Family
@param view: should be an instance of FamilyEditorView
'''
super(FamilyEditorPresenter, self).__init__(model, view)
self.session = object_session(model)
# initialize widgets
self.init_enum_combo('fam_qualifier_combo', 'qualifier')
self.synonyms_presenter = SynonymsPresenter(self.model, self.view,
self.session)
self.refresh_view() # put model values in view
# connect signals
self.assign_simple_handler('fam_family_entry', 'family')
self.assign_simple_handler('fam_qualifier_combo', 'qualifier')
self.assign_simple_handler('fam_notes_textview', 'notes')
# for each widget register a signal handler to be notified when the
# value in the widget changes, that way we can do things like sensitize
# the ok button
self.__dirty = False
def set_model_attr(self, field, value, validator=None):
#debug('set_model_attr(%s, %s)' % (field, value))
super(FamilyEditorPresenter, self).set_model_attr(field, value,
validator)
self.__dirty = True
sensitive = self.model.family and True or False
self.view.set_accept_buttons_sensitive(sensitive)
def dirty(self):
return self.__dirty or self.synonyms_presenter.dirty()
def refresh_view(self):
for widget, field in self.widget_to_field_map.iteritems():
value = getattr(self.model, field)
self.view.set_widget_value(widget, value)
def start(self):
r = self.view.start()
return r
#
# TODO: you shouldn't be able to set a family as a synonym of itself
#
class SynonymsPresenter(editor.GenericEditorPresenter):
PROBLEM_INVALID_SYNONYM = 1
def __init__(self, family, view, session):
'''
@param model: Family instance
@param view: see GenericEditorPresenter
@param session:
'''
super(SynonymsPresenter, self).__init__(family, view)
self.session = session
self.init_treeview()
# use completions_model as a dummy object for completions, we'll create
# seperate SpeciesSynonym models on add
completions_model = FamilySynonym()
def fam_get_completions(text):
query = self.session.query(Family)
return query.filter(and_(Family.family.like('%s%%' % text),
Family.id != self.model.id))
self._selected = None
def on_select(value):
# don't set anything in the model, just set self._selected
sensitive = True
if value is None:
sensitive = False
self.view.widgets.fam_syn_add_button.set_sensitive(sensitive)
self._selected = value
self.assign_completions_handler('fam_syn_entry', fam_get_completions,
on_select=on_select)
self.view.connect('fam_syn_add_button', 'clicked',
self.on_add_button_clicked)
self.view.connect('fam_syn_remove_button', 'clicked',
self.on_remove_button_clicked)
self.__dirty = False
def dirty(self):
return self.__dirty
def init_treeview(self):
'''
initialize the gtk.TreeView
'''
self.treeview = self.view.widgets.fam_syn_treeview
# remove any columns that were setup previous, this became a
# problem when we starting reusing the glade files with
# utils.GladeLoader, the right way to do this would be to
# create the columns in glade instead of here
for col in self.treeview.get_columns():
self.treeview.remove_column(col)
def _syn_data_func(column, cell, model, iter, data=None):
v = model[iter][0]
cell.set_property('text', str(v))
# just added so change the background color to indicate its new
if v.id is None:
cell.set_property('foreground', 'blue')
else:
cell.set_property('foreground', None)
cell = gtk.CellRendererText()
col = gtk.TreeViewColumn('Synonym', cell)
col.set_cell_data_func(cell, _syn_data_func)
self.treeview.append_column(col)
tree_model = gtk.ListStore(object)
for syn in self.model._synonyms:
tree_model.append([syn])
self.treeview.set_model(tree_model)
self.view.connect(self.treeview, 'cursor-changed',
self.on_tree_cursor_changed)
def on_tree_cursor_changed(self, tree, data=None):
'''
'''
path, column = tree.get_cursor()
self.view.widgets.fam_syn_remove_button.set_sensitive(True)
def refresh_view(self):
"""
doesn't do anything
"""
return
def on_add_button_clicked(self, button, data=None):
'''
adds the synonym from the synonym entry to the list of synonyms for
this species
'''
syn = FamilySynonym(family=self.model, synonym=self._selected)
tree_model = self.treeview.get_model()
tree_model.append([syn])
self._selected = None
entry = self.view.widgets.fam_syn_entry
self.pause_completions_handler(entry, True)
entry.set_text('')
entry.set_position(-1)
self.pause_completions_handler(entry, False)
self.view.widgets.fam_syn_add_button.set_sensitive(False)
self.view.widgets.fam_syn_add_button.set_sensitive(False)
self.view.set_accept_buttons_sensitive(True)
self.__dirty = True
def on_remove_button_clicked(self, button, data=None):
'''
removes the currently selected synonym from the list of synonyms for
this species
'''
# TODO: maybe we should only ask 'are you sure' if the selected value
# is an instance, this means it will be deleted from the database
tree = self.view.widgets.fam_syn_treeview
path, col = tree.get_cursor()
tree_model = tree.get_model()
value = tree_model[tree_model.get_iter(path)][0]
# debug('%s: %s' % (value, type(value)))
s = Family.str(value.synonym)
msg = 'Are you sure you want to remove %s as a synonym to the ' \
'current family?\n\n<i>Note: This will not remove the family '\
'%s from the database.</i>' % (s, s)
if utils.yes_no_dialog(msg, parent=self.view.get_window()):
tree_model.remove(tree_model.get_iter(path))
self.model.synonyms.remove(value.synonym)
utils.delete_or_expunge(value)
self.session.flush([value])
self.view.set_accept_buttons_sensitive(True)
self.__dirty = True
class FamilyEditor(editor.GenericModelViewPresenterEditor):
label = 'Family'
mnemonic_label = '_Family'
# these have to correspond to the response values in the view
RESPONSE_OK_AND_ADD = 11
RESPONSE_NEXT = 22
ok_responses = (RESPONSE_OK_AND_ADD, RESPONSE_NEXT)
def __init__(self, model=None, parent=None):
'''
@param model: Family instance or None
@param parent: the parent window or None
'''
if model is None:
model = Family()
super(FamilyEditor, self).__init__(model, parent)
if not parent and bauble.gui:
parent = bauble.gui.window
self.parent = parent
self._committed = []
def handle_response(self, response):
'''
@return: return a list if we want to tell start() to close the editor,
the list should either be empty or the list of committed values, return
None if we want to keep editing
'''
not_ok_msg = 'Are you sure you want to lose your changes?'
if response == gtk.RESPONSE_OK or response in self.ok_responses:
try:
if self.presenter.dirty():
self.commit_changes()
self._committed.append(self.model)
except SQLError, e:
msg = _('Error committing changes.\n\n%s') % \
utils.xml_safe_utf8(e.orig)
utils.message_details_dialog(msg, str(e), gtk.MESSAGE_ERROR)
return False
except Exception, e:
msg = _('Unknown error when committing changes. See the ' \
'details for more information.\n\n%s') % \
utils.xml_safe_utf8(e)
utils.message_details_dialog(msg, traceback.format_exc(),
gtk.MESSAGE_ERROR)
return False
elif self.presenter.dirty() and utils.yes_no_dialog(not_ok_msg) or \
not self.presenter.dirty():
self.session.rollback()
return True
else:
return False
# respond to responses
more_committed = None
if response == self.RESPONSE_NEXT:
self.presenter.cleanup()
e = FamilyEditor(parent=self.parent)
more_committed = e.start()
elif response == self.RESPONSE_OK_AND_ADD:
e = GenusEditor(Genus(family=self.model), self.parent)
more_committed = e.start()
if more_committed is not None:
if isinstance(more_committed, list):
self._committed.extend(more_committed)
else:
self._committed.append(more_committed)
return True
def start(self):
self.view = FamilyEditorView(parent=self.parent)
self.presenter = FamilyEditorPresenter(self.model, self.view)
# add quick response keys
dialog = self.view.dialog
self.attach_response(dialog, gtk.RESPONSE_OK, 'Return',
gtk.gdk.CONTROL_MASK)
self.attach_response(dialog, self.RESPONSE_OK_AND_ADD, 'k',
gtk.gdk.CONTROL_MASK)
self.attach_response(dialog, self.RESPONSE_NEXT, 'n',
gtk.gdk.CONTROL_MASK)
while True:
response = self.presenter.start()
self.view.save_state() # should view or presenter save state
if self.handle_response(response):
break
self.presenter.cleanup()
self.session.close() # cleanup session
return self._committed
#
# Family infobox
#
from bauble.view import InfoBox, InfoExpander, PropertiesExpander, \
select_in_search_results
import bauble.paths as paths
from bauble.plugins.plants.genus import Genus
from bauble.plugins.plants.species_model import Species
class GeneralFamilyExpander(InfoExpander):
'''
generic information about an family like number of genus, species,
accessions and plants
'''
def __init__(self, widgets):
'''
the constructor
'''
InfoExpander.__init__(self, _("General"), widgets)
general_box = self.widgets.fam_general_box
self.widgets.remove_parent(general_box)
self.vbox.pack_start(general_box)
def update(self, row):
'''
update the expander
@param row: the row to get the values from
'''
self.set_widget_value('fam_name_data', '<big>%s</big>' % row)
session = bauble.Session()
# get the number of genera
ngen = session.query(Genus).filter_by(family_id=row.id).count()
self.set_widget_value('fam_ngen_data', ngen)
# get the number of species
nsp = session.query(Species).join('genus').\
filter_by(family_id=row.id).count()
if nsp == 0:
self.set_widget_value('fam_nsp_data', 0)
else:
ngen_in_sp = session.query(Species.genus_id).\
join(['genus', 'family']).\
filter_by(id=row.id).distinct().count()
self.set_widget_value('fam_nsp_data', '%s in %s genera' \
% (nsp, ngen_in_sp))
# stop here if no GardenPlugin
if 'GardenPlugin' not in pluginmgr.plugins:
return
# get the number of accessions in the family
from bauble.plugins.garden.accession import Accession
from bauble.plugins.garden.plant import Plant
nacc = session.query(Accession).join(['species', 'genus', 'family']).\
filter_by(id=row.id).count()
if nacc == 0:
self.set_widget_value('fam_nacc_data', nacc)
else:
nsp_in_acc = session.query(Accession.species_id).\
join(['species', 'genus', 'family']).\
filter_by(id=row.id).distinct().count()
self.set_widget_value('fam_nacc_data', '%s in %s species' \
% (nacc, nsp_in_acc))
# get the number of plants in the family
nplants = session.query(Plant).\
join(['accession', 'species', 'genus', 'family']).\
filter_by(id=row.id).count()
if nplants == 0:
self.set_widget_value('fam_nplants_data', nplants)
else:
nacc_in_plants = session.query(Plant.accession_id).\
join(['accession', 'species', 'genus','family']).\
filter_by(id=row.id).distinct().count()
self.set_widget_value('fam_nplants_data', '%s in %s accessions' \
% (nplants, nacc_in_plants))
session.close()
class SynonymsExpander(InfoExpander):
expanded_pref = 'infobox.family.synonyms.expanded'
def __init__(self, widgets):
InfoExpander.__init__(self, _("Synonyms"), widgets)
synonyms_box = self.widgets.fam_synonyms_box
self.widgets.remove_parent(synonyms_box)
self.vbox.pack_start(synonyms_box)
def update(self, row):
'''
update the expander
@param row: the row to get thevalues from
'''
syn_box = self.widgets.fam_synonyms_box
# remove old labels
syn_box.foreach(syn_box.remove)
# use True comparison in case the preference isn't set
self.set_expanded(prefs[self.expanded_pref] == True)
if len(row.synonyms) == 0:
self.set_sensitive(False)
else:
on_clicked = lambda l, e, syn: select_in_search_results(syn)
for syn in row.synonyms:
# create clickable label that will select the synonym
# in the search results
box = gtk.EventBox()
label = gtk.Label()
label.set_alignment(0, .5)
label.set_markup(Family.str(syn))
box.add(label)
utils.make_label_clickable(label, on_clicked, syn)
syn_box.pack_start(box, expand=False, fill=False)
self.show_all()
self.set_sensitive(True)
class NotesExpander(InfoExpander):
def __init__(self, widgets):
InfoExpander.__init__(self, _("Notes"), widgets)
notes_box = self.widgets.fam_notes_box
self.widgets.remove_parent(notes_box)
self.vbox.pack_start(notes_box)
def update(self, row):
if row.notes is None:
self.set_expanded(False)
self.set_sensitive(False)
else:
self.set_expanded(True)
self.set_sensitive(True)
self.set_widget_value('fam_notes_data', row.notes)
class LinksExpander(InfoExpander):
def __init__(self):
super(LinksExpander, self).__init__(_('Links'))
self.tooltips = gtk.Tooltips()
buttons = []
self.google_button = gtk.LinkButton("", _("Search Google"))
self.tooltips.set_tip(self.google_button, _("Search Google"))
buttons.append(self.google_button)
self.gbif_button = gtk.LinkButton("", _("Search GBIF"))
self.tooltips.set_tip(self.gbif_button,
_("Search the Global Biodiversity Information "\
"Facility"))
buttons.append(self.gbif_button)
self.itis_button = gtk.LinkButton("", _("Search ITIS"))
self.tooltips.set_tip(self.itis_button,
_("Search the Intergrated Taxonomic "\
"Information System"))
buttons.append(self.itis_button)
self.ipni_button = gtk.LinkButton("", _("Search IPNI"))
self.tooltips.set_tip(self.ipni_button,
_("Search the International Plant Names Index"))
buttons.append(self.ipni_button)
for b in buttons:
b.set_alignment(0, -1)
self.vbox.pack_start(b)
def update(self, row):
s = str(row)
self.gbif_button.set_uri("http://data.gbif.org/search/%s" % \
s.replace(' ', '+'))
itis_uri = "http://www.itis.gov/servlet/SingleRpt/SingleRpt?"\
"search_topic=Scientific_Name" \
"&search_value=%(search_value)s" \
"&search_kingdom=Plant" \
"&search_span=containing" \
"&categories=All&source=html&search_credRating=All" \
% {'search_value': s.replace(' ', '%20')}
self.itis_button.set_uri(itis_uri)
self.google_button.set_uri("http://www.google.com/search?q=%s" % \
s.replace(' ', '+'))
ipni_uri = "http://www.ipni.org/ipni/advPlantNameSearch.do?"\
"find_family=%s" \
"&find_isAPNIRecord=on& find_isGCIRecord=on" \
"&find_isIKRecord=on&output_format=normal" % s
self.ipni_button.set_uri(ipni_uri)
class FamilyInfoBox(InfoBox):
'''
'''
def __init__(self):
'''
'''
InfoBox.__init__(self)
glade_file = os.path.join(paths.lib_dir(), 'plugins', 'plants',
'infoboxes.glade')
self.widgets = utils.GladeWidgets(gtk.glade.XML(glade_file))
self.general = GeneralFamilyExpander(self.widgets)
self.add_expander(self.general)
self.synonyms = SynonymsExpander(self.widgets)
self.add_expander(self.synonyms)
self.notes = NotesExpander(self.widgets)
self.add_expander(self.notes)
self.links = LinksExpander()
self.add_expander(self.links)
self.props = PropertiesExpander()
self.add_expander(self.props)
if 'GardenPlugin' not in pluginmgr.plugins:
self.widgets.remove_parent('fam_nacc_label')
self.widgets.remove_parent('fam_nacc_data')
self.widgets.remove_parent('fam_nplants_label')
self.widgets.remove_parent('fam_nplants_data')
def update(self, row):
'''
'''
self.general.update(row)
self.synonyms.update(row)
self.notes.update(row)
self.links.update(row)
self.props.update(row)
__all__ = ['Family', 'FamilyEditor', 'FamilySynonym', 'FamilyInfoBox',
'family_context_menu', 'family_markup_func']
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